SMTL ID : 5l6i.2 (1 other biounit)

Uba1 in complex with Ub-MLN4924 covalent adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

hetero-1-2-mer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: R.21, N.478, R.481 Ligands: B39.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.478 Water bridges: A:R.481, A:R.481 Salt bridges: A:R.21, A:R.481

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: K.28, E.29 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: R.861 Chain B: R.74 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: R.202 Chain C: R.42, R.72 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.288 Ligands: GOL.14 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: L.114, V.117, D.136 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.554 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: L.134 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 9 residues within 4Å: Chain A: D.282, K.285, F.391, D.392, S.393, E.395, L.879, K.895, F.908 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.282, A:S.393, A:E.880 Water bridges: A:K.285, A:D.392, A:E.395, A:E.880 GOL.11: 3 residues within 4Å: Chain A: D.851, R.852, Q.853 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.852, A:Q.853 GOL.12: 10 residues within 4Å: Chain A: K.137, S.153, E.155, N.162, L.273, H.293, F.296, Q.297, H.300, Y.390 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.153, A:E.155, A:N.162, A:H.293 GOL.13: 4 residues within 4Å: Chain A: Y.24, E.180, K.854, F.857 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.24, A:E.180 GOL.14: 5 residues within 4Å: Chain A: R.288, N.344, D.346, L.347 Ligands: CL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.288, A:R.288, A:N.344 GOL.15: 7 residues within 4Å: Chain A: K.33, R.150, F.171, T.172, C.378, S.379, G.380 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.150, A:T.172, A:C.378, A:S.379 GOL.16: 6 residues within 4Å: Chain A: L.737, Y.740, V.819, N.828, H.829, H.830 No protein-ligand interaction detected (PLIP)

1 x B39: [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate(Covalent)

B39.17: 21 residues within 4Å: Chain A: G.441, G.443, A.444, D.470, N.471, D.472, R.481, Q.482, K.494, D.518, K.519, V.520, A.542, L.543, D.544, N.545, D.547, A.548, Y.551 Chain B: G.76 Ligands: SO4.1 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.543, A:A.548, A:Y.551 Hydrogen bonds: A:A.444, A:N.471, A:K.494, A:V.520, A:V.520, A:D.544, B:G.76 Water bridges: A:G.443, A:R.481, A:R.481 Salt bridges: A:R.481, A:K.494

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Misra, M. et al., Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme. Structure (2017)

Release Date

2017-06-14

Peptides

Ubiquitin-activating enzyme E1 1: A
Ubiquitin-40S ribosomal protein S31: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

Ubiquitin-activating enzyme E1 1

Ubiquitin-40S ribosomal protein S31

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